The papers cover theoretical or applied contributions that are motivated by a biological question focusing on modeling approaches, including process algebra, simulation approaches, analysis methods, in particular model checking and flux analysis, and case studies.

Qualitative Modeling and Simulation of Bacterial Regulatory Networks.- Integrated Analysis from Abstract Stochastic Process Algebra Models.- An Exact Brownian Dynamics Method for Cell Simulation.- Multiscale Modelling of Neuronal Signalling.- Systems Biology of Halophilic Archaea.- A Partial Granger Causality Approach to Explore Causal Networks Derived From Multi-parameter Data.- Functional Evolution of Ribozyme-Catalyzed Metabolisms in a Graph-Based Toy-Universe.- Component-Based Modelling of RNA Structure Folding.- A Language for Biochemical Systems.- The Attributed Pi Calculus.- The Continuous ?-Calculus: A Process Algebra for Biochemical Modelling.- Automatic Complexity Analysis and Model Reduction of Nonlinear Biochemical Systems.- Formal Analysis of Abnormal Excitation in Cardiac Tissue.- The Distribution of Mutational Effects on Fitness in a Simple Circadian Clock.- SED-ML – An XML Format for the Implementation of the MIASE Guidelines.- On Parallel Stochastic Simulation of Diffusive Systems.- Large-Scale Design Space Exploration of SSA.- Statistical Model Checking in BioLab: Applications to the Automated Analysis of T-Cell Receptor Signaling Pathway.- On a Continuous Degree of Satisfaction of Temporal Logic Formulae with Applications to Systems Biology.- A Model Checking Approach to the Parameter Estimation of Biochemical Pathways.- Compositional Definitions of Minimal Flows in Petri Nets.- On Inner and Outer Descriptions of the Steady-State Flux Cone of a Metabolic Network.- A Combinatorial Approach to Reconstruct Petri Nets from Experimental Data.- An Exact Brownian Dynamics Method for Cell Simulation.- Stochastic Analysis of Amino Acid Substitution in Protein Synthesis.- A Stochastic Single Cell Based Model of BrdU Measured Hematopoietic Stem CellKinetics.- Erratum: Analyzing a Discrete Model of Aplysia Central Pattern Generator.

This book constitutes the refereed proceedings of the 6th International Conference on Computational Methods in Systems Biology, CMSB 2008, held in Rostock, Germany, in September 2008. The 21 revised full papers presented together with the summaries of 5 invited papers were carefully reviewed and selected from more than 60 submissions. The papers cover theoretical or applied contributions that are motivated by a biological question focusing on modeling approaches, including process algebra, simulation approaches, analysis methods, in particular model checking and flux analysis, and case studies.

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